If you need to create a licence that has been agreed upon as a result of an opportunity, then go to Sales > Opportunities, access your opportunity by clicking the Opportunity Name (not the pencil icon).
Next, click New Licence, in the options menu on the right.
This will open the licence screen for you to complete.
Now simply go through the usual process of setting up a new client licence.
As soon as your Licence is activated, your Opportunity Stage should update to Checked In.